Hi Calin
It might be worth breaking down the circuit into chunks and testing each with simple Arduino programs, to track down possible hardware problems.
So, for example, write a short program or modify one of the Arduino example programs to flash each of the LEDs off and on. Disconnect all the other components from the Arduino (i.e. the potentiometers and the audio output) while doing this.
If this works OK for all LEDS, then reconnect each of the potentiometers in turn and make sure the LEDs still work ok.
Then use the Arduino example program ReadAnalogSerial to check that you are getting a changing (and sensible) reading from each potentiometer.
If this works ok, reconnect the audio output and retest LEDs and potentiometers. Then use one of the tone() example programs to see if you get audio through to your amp.
Cheers
Ray